Commit Graph

22421 Commits

Author SHA1 Message Date
Quincey Koziol
3290889de3
Dead code removal (#2690)
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.

* Committing clang-format changes

* Allow spaces (and tabs) in VOL connector info string from environment variable.

* Parse connector name from HDF5_PLUGIN_PATH environment variable better

* Correct H5VLquery_optional to use H5VL routine instead of H5I.  Also add an
error message to the failure return value from not finding a plugin.

* Play nice with existing plugin paths

* Use API routine to determine if native connector is terminal.

* Committing clang-format changes

* Make string size larger, to allow for connectors with longer names.

* Be more flexible about testing external pass through connectors, especially if
they have registered new optional operations.

* Dead code removal

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
2023-04-11 09:30:02 -07:00
Quincey Koziol
49a71463a0
Comment cleanup (#2689)
* Clean up content and redundant logging in comments.
2023-04-11 09:41:32 -05:00
Dana Robinson
1ad030f669
Remove dead code hidden behind #ifdef LATER (#2686) 2023-04-10 11:39:46 -07:00
Allen Byrne
fc91e8856f
Fix #2598 sanitize leak (#2660) 2023-04-07 10:35:51 -07:00
Allen Byrne
526f0769a3
Minor fixes for CMake code and install docs (#2623) 2023-04-03 14:38:10 -07:00
Allen Byrne
fa388e6ba4
Update java logger version (#2643) 2023-04-03 14:36:23 -07:00
jhendersonHDF
b8c27cec17
Minor fixes for Subfiling VFD tests (#2633) 2023-04-03 13:09:08 -05:00
jhendersonHDF
f105dcc20a
Synchronize HDF5 tests with VOL tests (#2628) 2023-04-03 13:08:39 -05:00
Dana Robinson
1c1af33a12
Fix memory leaks and aborts in H5O EFL decode (#2656)
* Convert asserts to error handling in efl decode

The function that decodes external data files object header messages
would call assert() when parsing malformed files, causing applications
to crash when linked against the debug library.

This change converts these assert() calls to HDF5 error checks, so
the messages are sanity checked in both release and debug mode and
debug mode no longer crashes applications.

Also cleaned up some error handling usage and debug checks.

* Free memory on H5O efl decode errors

* Add buffer size checks to efl msg decode

* Add parentheses to math expressions

Fixes GitHub #2605
2023-04-03 11:06:36 -07:00
jhendersonHDF
7b426bf3ea
CMake - Match Autotools behavior for library instrumentation (#2648)
Enable library instrumentation by default for parallel debug builds
2023-03-31 22:38:15 -05:00
H. Joe Lee
879575f3fa
chore: make comment consistent (#2654)
Use a 3rd person verb to match "Does not" in the next sentence.
2023-03-31 22:37:12 -05:00
jhendersonHDF
d3d1a03f2c
Avoid suppressing error output for non-tentative file opens (#2632)
* Avoid suppressing error output for non-tentative file opens

* Update comment about tentative file opens
2023-03-31 22:36:28 -05:00
jhendersonHDF
31c26e72c5
Fix a memory corruption issue in H5S__point_project_simple (#2626) 2023-03-23 22:55:34 -05:00
Dana Robinson
7fd9a4435f
Fix minor things noted when doing 1.10 merges (#2610)
* Duplicated HDF_RESOURCES_DIR from cmake_ext_mod merge
* Typos in comments
2023-03-23 22:55:18 -05:00
Dana Robinson
af2666013f
Bring new release_docs scheme from 1.14 (#2614) 2023-03-22 18:41:00 -07:00
Dana Robinson
7b5e67b066
Fix test script names in cleanup code (#2590)
When the test scripts were renamed, DISTCLEANFILES in Makefile.am
was not updated.
2023-03-20 08:04:27 -07:00
jhendersonHDF
1392b9fc17
Subfiling VFD - fix issues with I/O concentrator selection strategies (#2571)
Fix multiple bugs with the SELECT_IOC_EVERY_NTH_RANK and
SELECT_IOC_TOTAL I/O concentrator selection strategies and add a
regression test for them
2023-03-17 15:45:07 -05:00
Dana Robinson
549fbcba86
Add a clang-format comment about permissions (#2577) 2023-03-17 12:56:14 -05:00
Dana Robinson
a89f1a4d75
Remove an obsolete comment from the MDS test (#2578)
The seed is now broadcast from rank 0, so the warning about multiple
machines having different seeds is unnecessary.
2023-03-17 12:55:32 -05:00
Mark Kittisopikul
f35a99e4e6
Fix 2nd argument of Java H5Fis_accessible (#2535) 2023-03-17 12:25:56 -05:00
glennsong09
dfa4d550de
Enclose MESG in do...while loop (#2576)
Enclose MSG macro in a do...while loop
2023-03-17 09:41:54 -07:00
Allen Byrne
2ca2a300ac
Change libaec URL to actively maintained repo GH#2552 (#2559) 2023-03-15 18:48:54 -05:00
Dana Robinson
469a93790e
Rename clang-format fix action (#2550)
The clang-format fix and check actions have the same name. This
also makes some small changes to the action's text fields.
2023-03-14 00:57:38 -07:00
Dana Robinson
19a9b12eea
Add Glenn Song to the CODEOWNERS file (#2551)
Also removes Ray Lu
2023-03-14 00:57:19 -07:00
Allen Byrne
cb679af19d
Make sure that ONLY_SHARED_LIBS option is correctly set (#2544) 2023-03-13 16:24:49 -05:00
Scot Breitenfeld
3d8dc012a4
Add concurrency option to cancel in-progress jobs (#2539) 2023-03-13 16:24:15 -05:00
Allen Byrne
42d1e89755
GH issue #1142, print must have verbose on first (#2540) 2023-03-13 16:23:33 -05:00
Scot Breitenfeld
d2345e9f0c
Addressed various Doxygen grammar issues. (#2524)
* reviewed H5A

* Addressed various grammar issues.

* remove double words, spelling fixes

* replace the use of rawdata with raw data
2023-03-13 11:53:08 -05:00
Mark (he/his) C. Miller
befbbd0b6d
Elaborate how cd_values get stored (#2522) 2023-03-08 16:46:10 -06:00
H. Joe Lee
d6f931d67b
docs: in -> out (#2514) (#2516) 2023-03-08 15:09:06 -06:00
mattjala
4b7bdfec69
Update ReferenceManual.dox (#2517) 2023-03-08 15:08:04 -06:00
Mark Kittisopikul
04682f2788
Fix H5Dchunk_iter doxygen example, cherry-pick of ef3bed6 (#2519) 2023-03-08 15:06:17 -06:00
Mark Kittisopikul
9884e189ac
Remove redundant and flawed documentation of H5D_chunk_iter_op_t from H5D.c (#2512)
Forward port of 9f252f1 from #2329
2023-03-08 14:46:47 -06:00
Mark Kittisopikul
5d3d43b1ee
Fix new codespell issues (#2521)
* Fix new codespell issues

* Have codespell ignore ./config/sanitizer/sanitizers.cmake
2023-03-08 14:42:47 -06:00
Allen Byrne
7b833f04b5
Update cross compile checks and files (#2497) 2023-03-02 11:18:13 -06:00
Egbert Eich
b16ec83d4b
Check for overflow when calculating on-disk attribute data size (#2459)
* Remove duplicate code

Signed-off-by: Egbert Eich <eich@suse.com>

* Add test case for CVE-2021-37501

Bogus sizes in this test case causes the on-disk data size
calculation in H5O__attr_decode() to overflow so that the
calculated size becomes 0. This causes the read to overflow
and h5dump to segfault.
This test case was crafted, the test file was not directly
generated by HDF5.
Test case from:
https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.md
2023-03-02 11:17:49 -06:00
Allen Byrne
877e4a67c5
Missing or misplaced entries in API reference tables #2470 (#2472)
* Missing or misplaced entries in API reference tables #2470

* Doxy corrections
2023-03-01 06:07:37 -08:00
Allen Byrne
d7128d144b
Add fetchcontent for compression libs and fix cmake config (#2487)
* Add fetchcontent for compression libs and fix cmake config

* MSDOS is a reserved define name

* Add release note and update install doc for FetchContent

* Add CI test for FetchContent

* Use LINK_COMP_LIBS instead of STATIC_LIBRARY for depends

* Use general link
2023-02-26 15:06:14 -08:00
jhendersonHDF
49fdba1091
Subfiling VFD - add option to specify config file prefix (#2495) 2023-02-26 10:12:00 -08:00
raylu-hdf
ea5b3952f7
HDFFV-10368 (OESS-319): Making two useful macros (H5L_EXT_FLAGS_ALL and H5L_EXT_VERSION) public (#2386)
* HDFFV-10368 (OESS-319): Move two useful macros (H5L_EXT_FLAGS_ALL and H5L_EXT_VERSION) from H5Lpkg.h to H5Lpublic.h for public usage. The test in vol.c only envokes H5Lcreate_external using the passthru VOL.  To test if the macros are public, one can use them in the link creation of the passthru VOL, such as printing out their values.

* Committing clang-format changes

* Moved the test for the external link public macros (H5L_EXT_FLAGS_ALL and H5L_EXT_VERSION) from vol.c to links.c.

* Committing clang-format changes

* Minor change: changed a pointer variable to an integer.

* Committing clang-format changes

* Moved two macros (H5L_EXT_VERSION and H5L_EXT_FLAGS_ALL) to H5Ldevelop.h for only developers to use.

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-02-21 08:38:00 -08:00
Allen Byrne
7ff3eac667
Remove space from toolchain name (#2482)
* Remove space from toolchain name

* Another space removed
2023-02-21 06:24:53 -08:00
raylu-hdf
7be4e913a8
OESS-330/HDFFV-11282: Improve failure message when a VOL connector can't be loaded (#2481)
* OESS-330/HDFFV-11282: Improve failure message when a VOL connector can't be loaded.  Made the error message clearer when the library can't find a plugin in the path table that contains the paths set by HDF5_PLUGIN_PATH and the default location and maybe set by H5PLxxx functions.

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-02-20 08:53:52 -06:00
jhendersonHDF
b3da28b731
Fix issue with collective metadata writes of global heap data (#2480) 2023-02-20 08:49:34 -06:00
Allen Byrne
bfef9945a8
Develop toolchain lowercase names and updates (#2426)
* lowercase the toolchain filenames

* Change name of option define

* Update CI with changed toolchain name

* Correct Intel compiler names

* Account for Intels name for compiler based on clang

* Make icx default and rename classic to icc
2023-02-17 14:37:26 -08:00
Allen Byrne
32a54c0e2e
CMake generated pkg-config file is incorrect #2259 (#2476)
* CMake generated pkg-config file is incorrect #2259

* Fix fortran pc template

* hdf5.pc is incorrect for debug builds #1546

* Correct pkg name and lib name

* Fix typo

* Fix missing space
2023-02-17 14:17:17 -08:00
raylu-hdf
0cc028a36c
GitHub #2417: to avoid the pass-through VOL failing in unexpected places, make sure the underneath VOL ID is specified. (#2475)
* GitHub #2417: to avoid the pass-through VOL failing in unexpected places, make sure the underneath VOL ID is specified.

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-02-17 14:15:48 -08:00
Allen Byrne
966454aac1
Add build options for CMake packaging #2347 (#2462) 2023-02-15 11:11:42 -06:00
Dana Robinson
6e3b34188e
Add parallel Autotools -Werror checks (#2384)
New actions added to GitHub CI to build parallel HDF5 w/ CFLAGS=-Werror. Since the GitHub runners are so underpowered, we just configure, build, and install but do not run tests. This covers Autotools only, both debug and release.
2023-02-13 11:57:43 -08:00
Dana Robinson
5ce275145c
Fix uninitialized variable in pio_engine.c (#2463) 2023-02-13 10:36:17 -08:00
Dana Robinson
02b93cad26
Fix a possible uninitialized variable in pio_perf (#2461) 2023-02-13 08:10:47 -08:00